[Freesurfer] Use of separate manual segmentation for hippocampus formation

Hi Freesurfer Experts and Advisors, Would it be possible to use different manually segmented images (of the hippocampus formation only) as a-priori maps and then use Freesurfer to automatically segment the hippocampus formation only, based on the furnished manually segmented images? This would be

Re: [Freesurfer] QDEC Analysis of only one group

Thank you Prof. Greve. Hope all is well on your side. On Thu, Jun 14, 2012 at 8:03 PM, Douglas N Greve wrote: > It is okay to study a single cohort with covariates. > doug > > On 06/14/2012 11:54 AM, Dhinakaran Chinappen wrote: > > Dear Freesurfer Experts, > > > >

[Freesurfer] QDEC Analysis of only one group

Dear Freesurfer Experts, For one of our studies, I have used QDEC to analyze the relationship between cortical thickness and a series of variables. I wanted to double check to see if it is okie to have a qdec table which only includes the diseased population and the covariates (such as FSIQ). Af

[Freesurfer] Definition of Surface Area Metric

Dear Freesurfer Experts, Would you mind clarifying what the measure of surface area anatomically means? Is it the area of the pial surface? Thanks in advance, Dhinakaran. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.ha

[Freesurfer] Cortical GM in aseg.stats vs. aparc.stats

Dear all, If I sum up the Gray Matter Volume (GrayVol) in aparc.stats for left (or right) hemisphere for all the regions, am I expecting that number to be different from the volume of the Left-Cerebral-Cortex (or Right-Cerebral-Cortex)? Am I correct in assuming that Left-Cerebral-Cortex is the sa

[Freesurfer] Total WM and GM Vol in FS 5.0.0

Hi all, I am using Freesurfer 5.0.0, before the outputs for cortical and subcortical GM and WM were made available in the final output files. What is the best way to calculate total gray matter volume (cortical and subcortical)? Is it through mris_anatomical_stats or mri_segstats? Also, are there

[Freesurfer] White Matter question

Dear all, I was wondering if you have encountered this issue before: Would you anticipate a difference between the volume calculated by Freesurfer 5.0 in Cerebral-White-Matter volume and the total volume calculated from the regions (defined by the Desikan atlas) in wmparc.stats? In one of my stu

[Freesurfer] qcache

Dear Freesurfer(ers). Quick ques: is it possible to run recon-all with the qcache flag during the initial reconstruction, as opposed to re-using recon-all with the qcache flag afterwards? Thanks, Dhinakaran. ___ Freesurfer mailing list Freesurfer@nmr.mg

[Freesurfer] Basal Ganglia Components

Dear all, Hope your research is going smoothly. My question refers to the basal ganglai components. I previously shot an email which Prof. Fischl was kind enough to reply to: the basal ganglia is not computed as a structure of its own in FreeSurfer. These are the structures of the basal ganglia

[Freesurfer] Basal Ganglia

Dear all, I was wondering if there is a direct measurement to get the basal ganglia volume? I looked into the stats files but could get my hands on it. Is there a particular calculation to carry out? Thanks in advance, Dhinakaran Chinappen